But, looking back at RGBYFRLG and some minor instances in Emerald and Crystal...there could be material to work with in order to create more story for Mewtwo.
In RGBYFRLG we're introduced to the character of Dr. Fuji through the old journals in Cinnabar Island. This journals chronicle the creation of Mewtwo.
Pokemon Emerald, in the island where you can find Mew, there are this incomplete writtings that point to Dr. Fuji.
In Pokemon Crystal, where Mewtwo was located 3 years prior in RGBY, there's an item found called the Bezerk Gene. This item hasn't been introduced to the games since Gen II. (Though this was basically retconned in HGSS.)
What am I getting at? There's a story that could possibly be expanded upon already within game canon and an item that was basically retconned out of continuity that could possibly find it's way back in through a new explanation. A new explanation in part being what we expect for all this "Newtwo" thing to make sense.
But. I will say this, around is floating the idea that if this is a new Pokemon, that it could've been created as a mass produced dumbed down version of Mewtwo. Which I really wouldn't mind.